I don't use the vapor trail, but it's lighter cousin, the virga - I simply load a platypus bag into the main compartment in the middle near my back, and run the hose out the top, run it through and clip to the sternum strap.

OTOH, I have successfully carried a 600 ml (20 oz) coke bottle just fine in the bottom side pocket
with the pack full, and it seems pretty secure - and when I look at it the pockets appear to be the same as those on the vapour trail. A coke bottle appears pretty secure in there, I don't think something a fat as a nalgene would be - it is a bit to tight and short for that. The narrowness of the coke bottle and the tapered waist of it seems to help make it work ok.

My problem with that for what you are suggesting is that I have trouble reaching the bottle without taking the pack off at that point.